Structure of PDB 4ngr Chain A Binding Site BS01

Receptor Information
>4ngr Chain A (length=689) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KHNMKAFLDELKAENIKKFLYNFTQIPHLAGTEQNFQLAKQIQSQWKEFG
LDSVELAHYDVLLSYPNKTHPNYISIINEDGNEIFNTSLFEPPPPGYENV
SDIVPPFSAFSPQGMPEGDLVYVNYARTEDFFKLERDMKINCSGKIVIAR
YGKVFRGNKVKNAQLAGAKGVILYSDPADYFAPGVKSYPDGWNLPGGGVQ
RGNILNLNGAGDPLTPGYPANEYAYRRGIAEAVGLPSIPVHPIGYYDAQK
LLEKMGGSAPPDSSWRGSLKVPYNVGPGFTGNFSTQKVKMHIHSTNEVTR
IYNVIGTLRGAVEPDRYVILGGHRDSWVFGGIDPQSGAAVVHEIVRSFGT
LKKEGWRPRRTILFASWDAEEFGLLGSTEWAEENSRLLQERGVAYINADS
SIEGNYTLRVDCTPLMYSLVHNLTKELKSPDEGFEGKSLYESWTKKSPSP
EFSGMPRISKLGSGNDFEVFFQRLGIASGRARYTKNGYPLYHSVYETYEL
VEKFYDPMFKYHLTVAQVRGGMVFELANSIVLPFDCRDYAVVLRKYADKI
YSISMKHPQEMKTYSVSFDSLFSAVKNFTEIASKFSERLQDFDKSNPIVL
RMMNDQLMFLERAFIDPLGLPDRPFYRHVIYAPSSHNKYAGESFPGIYDA
LFDIESKVDPSKAWGEVKRQIYVAAFTVQAAAETLSEVA
Ligand information
Ligand IDJ21
InChIInChI=1S/C23H31BrN4O10/c1-13(29)25-10-11-38-18-12-14(24)5-6-15(18)20(32)26-9-3-2-4-16(21(33)34)27-23(37)28-17(22(35)36)7-8-19(30)31/h5-6,12,16-17H,2-4,7-11H2,1H3,(H,25,29)(H,26,32)(H,30,31)(H,33,34)(H,35,36)(H2,27,28,37)/t16-,17-/m0/s1
InChIKeyGEZLVAJRFLXCLD-IRXDYDNUSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(=O)NCCOc1cc(Br)ccc1C(=O)NCCCC[CH](NC(=O)N[CH](CCC(O)=O)C(O)=O)C(O)=O
OpenEye OEToolkits 1.7.6CC(=O)NCCOc1cc(ccc1C(=O)NCCCC[C@@H](C(=O)O)NC(=O)N[C@@H](CCC(=O)O)C(=O)O)Br
OpenEye OEToolkits 1.7.6CC(=O)NCCOc1cc(ccc1C(=O)NCCCCC(C(=O)O)NC(=O)NC(CCC(=O)O)C(=O)O)Br
CACTVS 3.385CC(=O)NCCOc1cc(Br)ccc1C(=O)NCCCC[C@H](NC(=O)N[C@@H](CCC(O)=O)C(O)=O)C(O)=O
ACDLabs 12.01O=C(c1c(OCCNC(=O)C)cc(Br)cc1)NCCCCC(C(=O)O)NC(=O)NC(C(=O)O)CCC(=O)O
FormulaC23 H31 Br N4 O10
NameN-{[(1S)-5-({2-[2-(acetylamino)ethoxy]-4-bromobenzoyl}amino)-1-carboxypentyl]carbamoyl}-L-glutamic acid
ChEMBLCHEMBL3309676
DrugBank
ZINCZINC000098209034
PDB chain4ngr Chain A Residue 814 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4ngr Rational design of urea-based glutamate carboxypeptidase II (GCPII) inhibitors as versatile tools for specific drug targeting and delivery.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		K207 R210 N257 E424 L428 R463 G518 N519 R534 R536 G548 Y552 H553 N698 K699 Y700
Binding residue
(residue number reindexed from 1)		K153 R156 N203 E370 L374 R409 G464 N465 R480 R482 G487 Y491 H492 N637 K638 Y639
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.55,Ki=28.1nM
BindingDB: Ki=0.268000nM
Enzymatic activity
Enzyme Commision number 3.4.17.21: glutamate carboxypeptidase II.
Gene Ontology
Molecular Function
GO:0004180 carboxypeptidase activity
GO:0004181 metallocarboxypeptidase activity
GO:0008233 peptidase activity
GO:0008237 metallopeptidase activity
GO:0016805 dipeptidase activity
GO:0046872 metal ion binding
GO:1904492 Ac-Asp-Glu binding
GO:1904493 tetrahydrofolyl-poly(glutamate) polymer binding
Biological Process
GO:0006508 proteolysis
GO:0006760 folic acid-containing compound metabolic process
GO:0035609 C-terminal protein deglutamylation
Cellular Component
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0009986 cell surface
GO:0016020 membrane
GO:0070062 extracellular exosome

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4ngr, PDBe:4ngr, PDBj:4ngr
PDBsum4ngr
PubMed24954515
UniProtQ04609|FOLH1_HUMAN Glutamate carboxypeptidase 2 (Gene Name=FOLH1)

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